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GitHub Actions: add TODO statement to encourage customisation #488

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Merged
drpatelh merged 2 commits into from
Jan 27, 2020
Merged

GitHub Actions: add TODO statement to encourage customisation #488

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GitHub Actions: add TODO statement to encourage customisation
ewels Jan 27, 2020
986879e
Update ci.yml
drpatelh Jan 27, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@
* Fixed global environment variable in GitHub actions CI workflow
* Add `--awscli` parameter
* Fix buggy ANSI codes in pipeline summary log messages
* Add a `TODO` line in the new GitHub Actions CI test files

### Base Docker image

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14 changes: 8 additions & 6 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/ci.yml
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@@ -1,27 +1,29 @@
name: nf-core CI
# This workflow is triggered on pushes and PRs to the repository.
# It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on: [push, pull_request]
on: [push, pull_request]

jobs:
test:
env:
env:
NXF_VER: {% raw %}${{ matrix.nxf_ver }}{% endraw %}
NXF_ANSI_LOG: false
runs-on: ubuntu-18.04
runs-on: ubuntu-latest
strategy:
matrix:
# Nextflow versions: check pipeline minimum and current latest
nxf_ver: ['19.10.0', '']
steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Pull image
- name: Pull docker image
run: |
docker pull {{ cookiecutter.name_docker }}:dev && docker tag {{ cookiecutter.name_docker }}:dev {{ cookiecutter.name_docker }}:dev
- name: Run test
- name: Run pipeline with test data
run: |
# TODO nf-core: You can customise CI pipeline run tests as required
# (eg. adding multiple test runs with different parameters)
nextflow run ${GITHUB_WORKSPACE} -profile test,docker